Innervated organoid compositions and methods of making same

ABSTRACT

Disclosed are in vitro methods for the differentiation of precursor cells into a neural crest cell (NCC) primed to a neurogenic lineage. The methods may include, for example, the steps of activating a Hedgehog signaling pathway (“HH signaling pathway”) in a precursor cell, wherein the precursor cell may be contacted with a neural crest cell induction medium for differentiation of the precursor cell into a neural crest cell. Compositions for carrying out the disclosed methods are also disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of and priority to U.S. Provisional Patent application U.S. Ser. No. 62/799,818, entitled “Innervated Organoid Compositions and Methods of Making Same” which is incorporated by reference in its entirety for all purposes.

BACKGROUND

The neural crest (NC) is a transient population of multipotent progenitor cells in vertebrates, contributing to the formation of various organ systems. Aberrant NC development results in a myriad of birth defects and diseases. Directed differentiation protocols for derivation of NC from human pluripotent stem cells (hPSCs) have been established by various research groups and used for disease modeling and regenerative medicine (Fattahi et al., 2016; Lai et al., 2017; Lee et al., 2010; Menendez et al., 2013). However, the effort was made mainly for the generation of various subtypes of NC or improving the NC yield, and increasing their ability to generate functional neurons with high reproducibility across hPSC lines remains an important challenge.

The existing protocols to differentiate hPSC into NC are mainly based on the modulation of the known inductive signals implicated in early NC development. For instance, hPSCs are first directed to the neuroectoderm lineage through inhibition of the BMP and TGFβ pathways. Subsequent activation of the WNT pathway allows the generation of NC, while addition of retinoic acid can default cells toward the posterior NC fate and generates NC cells that express posterior HOX codes (Fattahi et al., 2016; Liu et al., 2015; Munera et al., 2017). Overall, it is a robust and widely used approach for the generation of NC cells with distinct fate potentials along various axial levels. However, NC cells obtained through this approach are usually heterogeneous, and their neurogenic potential varies across different hPSC lines, a problem that may necessitate the addition of other factor(s) to further boost the neurogenic fate potential of these cells. Currently, there is very limited understanding of the molecular events underlying the hPSC-to-NC transition and their subsequent neuronal lineage differentiation. It is also unclear whether manipulation of other developmental pathways known to act during the later stage of NC development will improve the speed and efficiency of neural fate acquisition.

In particular, the generation of various subtypes of neural crest (NC) or improving the neural crest yield from precursor cells, and increasing their ability to generate functional neurons with high reproducibility across hPSC lines remains an important challenge. Thus, there is a need in the art for improved methods for generating of functioning cells such as neural crest cells from a precursor cell, and the resulting functioning cells. The instant disclosure seeks to address one or more of the aforementioned needs in the art.

BRIEF SUMMARY

Disclosed are methods of making organoids and/or human intestinal tissue containing a functional enteric nervous system (ENS) derived from precursor cells, more particularly induced pluripotent stem cells (iPSCs). Further disclosed are methods of differentiating iPSCs for the manufacture of organoids and/or human intestinal tissue containing a functional enteric nervous system and compositions for carrying out the disclosed methods.

BRIEF DESCRIPTION OF THE DRAWINGS

This application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

Those of skill in the art will understand that the drawings, described below, are for illustrative purposes only. The drawings are not intended to limit the scope of the present teachings in any way.

FIG. 1A-1G. Single-cell RNA-seq revealed several NC intermediates during the hPSC-to-NC transition. (1A) Derivation of NC from hPSCs. (1B) Left panel: t-SNE mapping of single-cell expression profiles. Right panel: Proliferation indexes of the 5 clusters identified in the hPSC-derived NC pool. (1C) Schematics of the three main developmental phases of NC. Violin plots show the expression of (1D) the stage-specific markers and (E) HOX genes in the 5 clusters. (1F) Predicted identity of each cluster. (1G) Violin plot shows the relative expression of four key HH pathway genes in the 5 clusters.

FIG. 2A-2G. Level of HH signaling affects the hPSC-to-NC transition. (2A & 2D) Schemes of SAG and cyclopamine treatments. Flow analysis of HNK-1⁺ p75^(NTR+) cells at day 10 of in vitro differentiation after (2B) SAG and (2E) cyclopamine treatments. (2C & 2F) Bar charts summarize the percentages of HNK-1⁺ p75^(NTR+) cells in 3 independent experiments. (2G) Complete removal of the activation domain of GLI3 was achieved by introducing a stop mutation in the exon 13 of GLI3 (red arrow). Western blot shows an absence of GLI3^(A) protein in GLI3^(Δ699/Δ699) hPSC-derived NC. Flow analysis of HNK-1⁺ p75^(NTR+) cells derived from the control (IMR90) and GLI3^(Δ699/Δ699)- hPSC lines. Quantitative data is shown in the bar chart.

FIG. 3A-3E. Biological pathways influenced by HH signaling during the hPSC-to-NC transition. (3A) Heatmap of Spearman correlations of transcriptomes between samples. (3B) Left panel: heatmap showing the differentially expressed genes (DEGs) in NC^(SAG0-10) and NC^(GLI3Δ699/Δ699). Right panel: Venn diagrams show DEGs that are up- or downregulated in both NC^(SAG0-10) and NC^(GLI3Δ699/Δ699). GO enrichment analysis: GO terms enriched in (3C) NC^(SAG0-10) and (3D) NC^(GLI3Δ699/Δ699). (3E) Volcano plot shows expression patterns of genes implicated in different biological pathways in NC^(SAG0-10) and NC^(GLI3Δ699/Δ699).

FIG. 4A-4H. High-resolution dissection of NC-to-neuron transition using scRNA-Seq. (4A) Scheme of derivation of NC and neurons from hPSC. (4B) t-SNE projection of all 1,538 individual cells during the whole differentiation process, colored by the indicated treatment groups. (4C) Visualization of the differentiation path using SPRING. (4D) Gene expression of key marker genes along the NC-to-neuron differentiation path confirms cell fate progression toward the neuronal lineage. (4E) Proliferation and migration indexes of the 8 clusters. (4F) Bar charts summarize the proportion of each cluster in different treatment groups. (4G) The expression dynamics of 425 top DEGs were cataloged into 3 major groups in a pseudotime manner, shown as blue lines (control) and red lines (SAG treatment group). Thick lines indicate the average gene expression patterns in each group. Gene Ontology (dark-colored bars) and KEGG pathway (light-colored bars) analyses of each gene group. (4H) Gene correlation network during NC-to-neuron transition. Green, orange and blue colors represent the key TFs uniquely expressed in each stage. Yellow stands for the TFs that are upregulated in the SAG treatment groups.

FIG. 5A-5D. Efficient derivation of peripheral dopaminergic and cholinergic neurons upon activation of HH signaling during the hPSC-to-NC transition. (5A) Scheme of neuronal lineage differentiation of the FACS-sorted NC cells. (5B) Immunocytochemistry analysis shows that NC^(SAG0-10) and NC^(GLI3Δ699/Δ699) express a marker of NC (SOX10), highly comparable to the control. (5C) NC^(GLI3Δ699/Δ699) underwent spontaneous neuronal differentiation and expressed pan-neuronal markers (HU & TUJ1). (5D) At day 21 of differentiation, control and NC^(SAG0-10) expressed various pan-neuronal markers (HU, TUJ1 & PGP9.5) and TH and VIP. Bar chart shows the quantitative data.

FIG. 6A-6E. hPSC-based human colonic organoid model for functional characterization. (6A) Schematic summarizes the differentiation protocol for the generation of HCOs+ENCCs. (6B) Formation of definitive endoderm (DE) after 3 days of culturing on endoderm differentiation medium. Immunocytochemistry analysis revealed that cells are definitive endoderm coexpressing the two endoderm markers FOXA2 and SOX17. (6C) Mid-/hindgut spheroids were cultured in Matrigel at day 28 Immunocytochemistry analysis revealed the presence of neuronal progenitors (TUJ1⁺), epithelium (CDH1), villi (VILLIN), colon (CA4) and goblet (MUC2) cells. (6D) Gross morphology of HCOs+ENCCs transplanted into the kidney subcapsular space of NOD/SCID mice for 11 weeks. Hematoxylin and eosin staining of colon tissue after transplantation. A neuronal marker (TUJ1, arrow) and a smooth muscle marker (SMA) show the presence of neurons between two smooth muscle layers and the presence of glial cells (S100b). Detection of the expression of markers for colon (CDX2, SATB2), goblet (MUC2) and endocrine (GLP-1) cells. (6E) HCOs and HCOs+ENCCs subjected to low-voltage electrical-field stimulation (EFS: 5-ms pulse at 30 V). HCOs+ENCCs showed a sustained series of wave-like contractions (lower panel) that were lost when tissues were cultured in TTX (lower right panel: 10 μM, 5 min).

FIG. 7A-7F. SAG treatment improves the neuromuscular coupling of ENCC-derived neurons. (7A) Immunocytochemistry analysis of Day 28 HCOs revealed more TUJ1⁺ and TH⁺ neurons in the SAG treatment group. (7B) Hematoxylin and eosin (H&E) staining of colon tissue after transplantation. Detection of the expression of markers for colon (CDX2, SATB2), goblet (MUC2) and endocrine (GLP-1) cells in the HCO+ENCC^(SAG0_10) explants. (7C) Immunohistochemistry detects the expression of markers for mature (PGP9.5, NF) and excitatory (CALRETININ) neurons, epithelium (CDH1) and muscle layer (SMA). (7D) Low-voltage electrical-field stimulation induced a more sustainable series of wave-like contractions with HCO+ENCCs^(SAG0_10). (7E) DMPP stimulation in HCO, HCO+ENCCs and HCO+SAG-ENCCs^(SAG0_10) in the absence or presence of TTX. (7F) Area under the curve (AUC) during DMPP (10 μM) stimulation measured for 2 min before and after stimulation (n=4 from two hPSC lines).

FIG. 8. Quality control for scRNA-seq data. (8A) Reads alignment ratio showing the number of mapped reads and unmapped reads in each cell. (8B) Sequencing saturation for the whole sequencing. With the increasing of the sequence depth, the detected gene number will reach the saturation (about 7500 genes). (8C) and (8D) Boxplots showing the difference of reads ount and detected gene number was found in control neurons.

FIG. 9. Gene expression heatmap of 425 top DEGs cataloged in eight clusters, in a pseudo-temporal order.

FIG. 10. Expression patterns of some key NC markers along the pseudotime.

FIG. 11. Differently expressed genes (DEGs) identified from Cluster 5 upon the SAG treatment.

FIG. 12. Metabolic related pathways were enriched in clusters 6 and 7. (A) the expression dynamics of 108 DEGs in Clusters 6&7. (B) GO (dark green) and KEGG (light green) annotation of the cluster 6&7 markers.

FIG. 13A-13C. The SAG treatment favors the ectoderm lineage differentiation. (13A) schematic shows SAG treatment strategy during the early phase of hPSC to NC transition. (12B) ectoderm lineage differentiation was monitored using immunocytochemistry (pluripotent stem cell: SOX2+ NANGO+; ectoderm: SOX2:NANGO−). (13C) Bar chart shows the percentage of SOX2+NANGO-cells in each treatment group.

FIG. 14A-14C. The SAG treatment promotes NC formation (14A) Schematic shows SAG treatment strategy during the early phase of hPSC to NC transition, (14B) immunocytochemistry was used to detect NC cells (SNAIL+). (14C) Bar chart shows the percentage of SNAIL+NC cells in each treatment group.

FIG. 15A-15C. The SAG treatment at the late stage of NC induction enhances the formation of TH+ neurons. (15A) schematic shows SAG treatment strategy during NC induction. (15B) immunocytochemistry was performed with pan-neuronal (TUJ1_ and subtype (TH) markers. (15C) Bar chart shows the percentage of TUJ1+ and TH+ neurons in each treatment group. “*” indicates significant difference from the constant (SAG 0-10) treatment group (P<0.05).

FIG. 16A-16C. Outlier detection for scRNA-seq (16A) Random outliers were added to public dataset (Pollen et al 2014) to check the effect of outliers on the correlation between true markers and non=markers. Results showing that, with the increase of outlier number, the correlation between true markers will severely decrease. (16B) public dataset (Deng, et al 2014) was modified to simulate the outliers. Only 1, 2, and 4 cells are retained for cluster 1, 2, and 3. Thus, cells in cluster 1 and 2 will become simulated outliers. The methods can robustly detect the simulated outliers and keep the rare cluster 3 (16C) mvoutlier fails to detect the simulated outliers.

FIG. 17A-17F. Comparison of three visualization methods on the scRNA-seq data. 1566 cells were visualized by three different methods (PCA, t-SNE and SPRING). (17A), (17C), and (17E) showing the 8 clusters, while (17B), (17D) and (17F) show the fourth cell groups. Both eight clusters and four cell groups can be clearly separated by three methods showing the effectiveness of the clustering result. Same pattern can be found in three methods.

FIG. 18. Differentiation protocol

DETAILED DESCRIPTION Definitions

Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art. In case of conflict, the present document, including definitions, will control. Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein may be used in practice or testing of the present invention. All publications, patent applications, patents and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting.

As used herein and in the appended claims, the singular forms “a,” “and,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a method” includes a plurality of such methods and reference to “a dose” includes reference to one or more doses and equivalents thereof known to those skilled in the art, and so forth.

The term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, e.g., the limitations of the measurement system. For example, “about” may mean within 1 or more than 1 standard deviation, per the practice in the art. Alternatively, “about” may mean a range of up to 20%, or up to 10%, or up to 5%, or up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term may mean within an order of magnitude, preferably within 5-fold, and more preferably within 2-fold, of a value. Where particular values are described in the application and claims, unless otherwise stated the term “about” meaning within an acceptable error range for the particular value should be assumed.

As used herein, the term “effective amount” means the amount of one or more active components that is sufficient to show a desired effect. This includes both therapeutic and prophylactic effects. When applied to an individual active ingredient, administered alone, the term refers to that ingredient alone. When applied to a combination, the term refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.

As used herein, the term “definitive endoderm (DE) cell” means one of the three primary germ layers produced by the process of gastrulation.

As used herein the term “wnt signaling pathway” means the wnt/beta-catenin pathway and is a signal transduction pathway that is mediated by Wnt ligands and frizzled cell surface receptors that acts through the beta-catenin protein.

As used herein the term “activator” with respect to a pathway, such as a “wnt pathway” means a substance that activates the Wnt/beta-catenin pathway such that Wnt/beta-catenin targets are increased.

As used herein, the term “FGF signaling pathway activator” means a substance that activates the FGF pathway such that FGF targets are increased.

As used herein, the term “BMP signaling pathway inhibitor” a substance that interferes with the BMP pathway and causes BMP targets to be decreased.

As used herein, the term “growth factor” means a substance capable of stimulating cellular processes including but not limited to growth, proliferation, morphogenesis or differentiation.

As used herein, the term “stable expression” of a marker means expression that does not change upon modification of the growth environment.

As used herein, the term “totipotent stem cells” (also known as omnipotent stem cells) are stem cells that can differentiate into embryonic and extra-embryonic cell types. Such cells can construct a complete, viable, organism. These cells are produced from the fusion of an egg and sperm cell. Cells produced by the first few divisions of the fertilized egg are also totipotent.

As used herein, the term “pluripotent stem cells (PSCs),” also commonly known as PS cells, encompasses any cells that can differentiate into nearly all cells, i.e., cells derived from any of the three germ layers (germinal epithelium), including endoderm (interior stomach lining, gastrointestinal tract, the lungs), mesoderm (muscle, bone, blood, urogenital), and ectoderm (epidermal tissues and nervous system). PSCs can be the descendants of totipotent cells, derived from embryos (including embryonic germ cells) or obtained through induction of a non-pluripotent cell, such as an adult somatic cell, by forcing the expression of certain genes.

As used herein, the term “induced pluripotent stem cells (iPSCs),” also commonly abbreviated as iPS cells, refers to a type of pluripotent stem cells artificially derived from a normally non-pluripotent cell, such as an adult somatic cell, by inducing a “forced” expression of certain genes.

As used herein, the term “precursor cell” encompasses any cells that can be used in methods described herein, through which one or more precursor cells acquire the ability to renew itself or differentiate into one or more specialized cell types. In some embodiments, a precursor cell is pluripotent or has the capacity to becoming pluripotent. In some embodiments, the precursor cells are subjected to the treatment of external factors (e.g., growth factors) to acquire pluripotency. In some embodiments, a precursor cell can be a totipotent stem cell; a pluripotent stem cell (induced or non-induced); a multipotent stem cell; and a unipotent stem cell. In some embodiments, a precursor cell can be from an embryo, an infant, a child, or an adult. In some embodiments, a precursor cell can be a somatic cell subject to treatment such that pluripotency is conferred via genetic manipulation or protein/peptide treatment.

In developmental biology, cellular differentiation is the process by which a less specialized cell becomes a more specialized cell type. As used herein, the term “directed differentiation” describes a process through which a less specialized cell becomes a particular specialized target cell type. The particularity of the specialized target cell type can be determined by any applicable methods that can be used to define or alter the destiny of the initial cell. Exemplary methods include but are not limited to genetic manipulation, chemical treatment, protein treatment, and nucleic acid treatment.

Pluripotent Stem Cells Derived from Embryonic Cells

In some embodiments, an important step is to obtain stem cells that are pluripotent or can be induced to become pluripotent. In some embodiments, pluripotent stem cells are derived from embryonic stem cells, which are in turn derived from totipotent cells of the early mammalian embryo and are capable of unlimited, undifferentiated proliferation in vitro. Embryonic stem cells are pluripotent stem cells derived from the inner cell mass of the blastocyst, an early-stage embryo. Methods for deriving embryonic stem cells from blastocytes are well known in the art. Human embryonic stem cells H9 (H9-hESCs) are used in the exemplary embodiments described in the present application, but it would be understood by one of skill in the art that the methods and systems described herein are applicable to any stem cells.

Additional stem cells that can be used in embodiments in accordance with the present invention include but are not limited to those provided by or described in the database hosted by the National Stem Cell Bank (NSCB), Human Embryonic Stem Cell Research Center at the University of California, San Francisco (UCSF); WISC cell Bank at the Wi Cell Research Institute; the University of Wisconsin Stem Cell and Regenerative Medicine Center (UW-SCRMC); Novocell, Inc. (San Diego, Calif.); Cellartis AB (Goteborg, Sweden); ES Cell International Pte Ltd (Singapore); Technion at the Israel Institute of Technology (Haifa, Israel); and the Stem Cell Database hosted by Princeton University and the University of Pennsylvania. Exemplary embryonic stem cells that can be used in embodiments in accordance with the present invention include but are not limited to SA01 (SA001); SA02 (SA002); ES01 (HES-1); ES02 (HES-2); ES03 (HES-3); ES04 (HES-4); ES05 (HES-5); ES06 (HES-6); BG01 (BGN-01); BG02 (BGN-02); BG03 (BGN-03); TE03 (13); TE04 (14); TE06 (16); UC01 (HSF1); UC06 (HSF6); WA01 (H1); WA07 (H7); WA09 (H9); WA13 (H13); WA14 (H14).

More details on embryonic stem cells can be found in, for example, Thomson et al., 1998, “Embryonic Stem Cell Lines Derived from Human Blastocysts,” Science 282 (5391):1145-1147; Andrews et al., 2005, “Embryonic stem (ES) cells and embryonal carcinoma (EC) cells: opposite sides of the same coin,” Biochem Soc Trans 33:1526-1530; Martin 1980, “Teratocarcinomas and mammalian embryogenesis,”. Science 209 (4458):768-776; Evans and Kaufman, 1981, “Establishment in culture of pluripotent cells from mouse embryos,” Nature 292(5819): 154-156; Klimanskaya et al., 2005, “Human embryonic stem cells derived without feeder cells,” Lancet 365 (9471): 1636-1641; each of which is hereby incorporated herein in its entirety.

Induced Pluripotent Stem Cells (iPSCs)

In some embodiments, iPSCs are derived by transfection of certain stem cell-associated genes into non-pluripotent cells, such as adult fibroblasts. Transfection is typically achieved through viral vectors, such as retroviruses. Transfected genes include the master transcriptional regulators Oct-3/4 (Pouf51) and Sox2, although it is suggested that other genes enhance the efficiency of induction. After 3-4 weeks, small numbers of transfected cells begin to become morphologically and biochemically similar to pluripotent stem cells, and are typically isolated through morphological selection, doubling time, or through a reporter gene and antibiotic selection. As used herein, iPSCs include but are not limited to first generation iPSCs, second generation iPSCs in mice, and human induced pluripotent stem cells. In some embodiments, a retroviral system is used to transform human fibroblasts into pluripotent stem cells using four pivotal genes: Oct3/4, Sox2, Klf4, and c-Myc. In alternative embodiments, a lentiviral system is used to transform somatic cells with OCT4, SOX2, NANOG, and LIN28. Genes whose expression are induced in iPSCs include but are not limited to Oct-3/4 (e.g., Pou5fl); certain members of the Sox gene family (e.g., Sox1, Sox2, Sox3, and Sox15); certain members of the Klf family (e.g., Klf1, Klf2, Klf4, and Klf5), certain members of the Myc family (e.g., C-myc, L-myc, and N-myc), Nanog, and LIN28.

In some embodiments, non-viral based technologies are employed to generate iPSCs. In some embodiments, an adenovirus can be used to transport the requisite four genes into the DNA of skin and liver cells of mice, resulting in cells identical to embryonic stem cells. Since the adenovirus does not combine any of its own genes with the targeted host, the danger of creating tumors is eliminated. In some embodiments, reprogramming can be accomplished via plasmid without any virus transfection system at all, although at very low efficiencies. In other embodiments, direct delivery of proteins is used to generate iPSCs, thus eliminating the need for viruses or genetic modification. In some embodiment, generation of mouse iPSCs is possible using a similar methodology: a repeated treatment of the cells with certain proteins channeled into the cells via poly-arginine anchors was sufficient to induce pluripotency. In some embodiments, the expression of pluripotency induction genes can also be increased by treating somatic cells with FGF2 under low oxygen conditions.

More details on embryonic stem cells can be found in, for example, Kaji et al., 2009, “Virus free induction of pluripotency and subsequent excision of reprogramming factors,” Nature 458:771-775; Woltjen et al., 2009, “piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells,” Nature 458:766-770; Okita et al., 2008, “Generation of Mouse Induced Pluripotent Stem Cells Without Viral Vectors,” Science 322(5903):949-953; Stadtfeld et al., 2008, “Induced Pluripotent Stem Cells Generated without Viral Integration,” Science 322(5903):945-949; and Zhou et al., 2009, “Generation of Induced Pluripotent Stem Cells Using Recombinant Proteins,” Cell Stem Cell 4(5):381-384; each of which is hereby incorporated herein in its entirety.

In some embodiments, exemplary iPS cell lines include but not limited to iPS-DF19-9; iPS-DF19-9; iPS-DF4-3; iPS-DF6-9; iPS(Foreskin); iPS(IMR90); and iPS(IMR90).

More details on the functions of signaling pathways relating to DE development can be found in, for example, Zorn and Wells, 2009, “Vertebrate endoderm development and organ formation,” Annu Rev Cell Dev Biol 25:221-251; Dessimoz et al., 2006, “FGF signaling is necessary for establishing gut tube domains along the anterior-posterior axis in vivo,” Mech Dev 123:42-55; McLin et al., 2007, “Repression of Wnt/β-catenin signaling in the anterior endoderm is essential for liver and pancreas development. Development,” 134:2207-2217; Wells and Melton, 2000, Development 127:1563-1572; de Santa Barbara et al., 2003, “Development and differentiation of the intestinal epithelium,” Cell Mol Life Sci 60(7): 1322-1332; each of which is hereby incorporated herein in its entirety.

Any methods for producing definitive endoderm from pluripotent cells (e.g., iPSCs or ESCs) are applicable to the methods described herein. In some embodiments, pluripotent cells are derived from a morula. In some embodiments, pluripotent stem cells are stem cells. Stem cells used in these methods can include, but are not limited to, embryonic stem cells. Embryonic stem cells can be derived from the embryonic inner cell mass or from the embryonic gonadal ridges. Embryonic stem cells or germ cells can originate from a variety of animal species including, but not limited to, various mammalian species including humans. In some embodiments, human embryonic stem cells are used to produce definitive endoderm. In some embodiments, human embryonic germ cells are used to produce definitive endoderm. In some embodiments, iPSCs are used to produce definitive endoderm.

The generation of fully functioning cells from human pluripotent stem cells (hPSCs) remains challenging. Here, Applicant has developed a method using differentiation cues to improve lineage manipulation of the transition from hPSC to neural crest (NC) cell to neuron at the single-cell level. Applicant found that Hedgehog (HH) signaling is activated in postmigratory NC-like cells and that activation of HH during the hPSC-to-NC transition robustly increased the NC yield, while suppression of HH by addition of an HH antagonist or constitutive expression of a repressor form of GLI3 abrogated this process and induced cell death. Single-cell transcriptomics analysis further revealed that activation of HH primes NC toward the neurogenic lineage. Intriguingly, in vitro cell and human innervated colonic organoid models further demonstrated that an HH agonist could augment the neuronal lineage differentiation of hPSC-derived NC, and this treatment greatly improved the functional competency of hPSC-derived neurons. In summary, Applicant established an experimental paradigm for systematically optimizing the differentiation protocol to generate functioning NC cells.

The neural crest (NC) is a transient population of multipotent progenitor cells in vertebrates, contributing to the formation of various organ systems. Aberrant NC development results in a myriad of birth defects and diseases. Directed differentiation protocols for derivation of NC from human pluripotent stem cells (hPSCs) have been established by various research groups and used for disease modeling and regenerative medicine (Fattahi et al., 2016; Lai et al., 2017; Lee et al., 2010; Menendez et al., 2013). However, the effort was made mainly for the generation of various subtypes of NC or improving the NC yield, and increasing their ability to generate functional neurons with high reproducibility across hPSC lines remains an important challenge.

The existing protocols to differentiate hPSC into NC are mainly based on the modulation of the known inductive signals implicated in early NC development. For instance, hPSCs are first directed to the neuroectoderm lineage through inhibition of the BMP and TGFβ pathways. Subsequent activation of the WNT pathway allows the generation of NC, while addition of retinoic acid can default cells toward the posterior NC fate and generates NC cells that express posterior HOX codes (Fattahi et al., 2016; Liu et al., 2015; Munera et al., 2017). Overall, it is a robust and widely used approach for the generation of NC cells with distinct fate potentials along various axial levels. However, NC cells obtained through this approach are usually heterogeneous, and their neurogenic potential varies across different hPSC lines, a problem that may necessitate the addition of other factor(s) to further boost the neurogenic fate potential of these cells. Currently, there is very limited understanding of the molecular events underlying the hPSC-to-NC transition and their subsequent neuronal lineage differentiation. It is also unclear whether manipulation of other developmental pathways known to act during the later stage of NC development will improve the speed and efficiency of neural fate acquisition.

The latest high-resolution RNA sequencing technology allows a comprehensive analysis of the lineage commitment process after the embryonic stem cells exit their pluripotent state and of the timing of various differentiation cues underlying the generation of cell type diversity (Semrau et al., 2017). In vitro NC derivation from hPSCs and their subsequent differentiation toward neuronal lineage involve multiple steps, and NC cells and their neuronal derivatives derived from hPSCs are likely heterogeneous, where cells at intermediate differentiation states may resemble NC cells at various developmental stages in vivo: these include NC cells that are residing at the neural plate border, undergoing specification and delamination, and fully committed to the neurogenic lineage (Sauka-Spengler and Bronner, 2010). Analyzing the transcriptomes of the hPSC-derived NC cells and their neuronal derivatives at the single-cell level may reveal the lineage-specifying signals underlying these developmental events and that information will guide optimization of the differentiation protocol for the generation of fully functioning NC in a systematic way.

Improving the neural fate differentiation efficiency of hPSC-derived NC cells will expedite the application of these cells in regenerative medicine, such as replenishing the missing neurons in the colon of patients with Hirschsprung (HSCR) disease. hPSC-derived organoids represent near-physiological models bridging in vitro research and clinical medicine. A protocol for the differentiation of human intestinal organoids (HIO) from hPSC was established recently (Workman et al., 2017). hPSC-derived HIOs contained all functional tissue units, including a functional enteric nervous system (ENS), and resembled native tissue architecture of the small intestine. In addition, human colonic organoids (HCOs) resembling the posterior bowel could be generated using a similar approach with a brief activation of the BMP pathway. Even though the reported HCOs did not contain ENS, these HCOs exhibited molecular, cellular and morphologic properties of the human colon (Munera et al., 2017). Taken together, the latest advances in organoid-based technologies raise an important possibility of using an innervated HCO model for appraising the therapeutic value of hPSC-derived NC cells.

The limited yield and immature differentiation of hPSC derivatives remain the major challenges for applications in regenerative medicine. Disclosed herein is a robust strategy for deriving NC from hPSCs by activating HH signaling during the NC induction. Together with a newly established innervated HCO model, Applicant has demonstrated that the disclosed methods significantly improve not only NC yield from hPSCs but also the differentiation capability of hPSC-derived NC to the neuronal lineage and the neuromuscular coupling of the neurons.

In one aspect, an in vitro method of differentiating a precursor cell into a neural crest cell primed to a neurogenic lineage is disclosed. The method may comprise the step of activating a Hedgehog signaling pathway (“HH signaling pathway”) in a precursor cell. The step may be combined with a neural crest cell induction medium. The activation step may be carried out, for example, for a period of time sufficient to differentiate the precursor cell into a neural crest cell. In one aspect, the precursor cell may be a pluripotent stem cell, for example, a human pluripotent stem cell. Surprisingly, the HH signaling level during the early phase of the hPSC-to-NC transition was found to determine the NC yield. Applicant's validation experiments indicated that a brief activation of HH pathway during the early phase of NC induction significantly enhances the ectoderm lineage commitment of hPSC and increases the number of SOX2+NANOG-cells at day 4 of differentiation. By “early phase” it is meant about 0 to about 4 days, and by “brief,” it is meant about 0 to about 2 days. If retinoic acid is added during the NC induction, posterior NCCs may be obtained, while anterior NCC may be obtained in absence of retinoic acid.

Any NCC induction media known in the art may be used for the disclosed protocol. In one aspect, the NCC induction media may comprise one or more growth factors, in particular, a SMAD pathway inhibitor, for example, dual SMAD inhibitors, LDN LDN193189 and SB431542. Both BMP and TGF signalling pathway will activate SMAD pathway. LDN192189 and SB431542 are the inhibitors (small molecules) for BMP and TGF signalling, respectively. Inhibition of BMP and TGF signalling pathways are crucial for ectoderm induction (for both CNS and neural crest) differentiation. The use of dual SMAD inhibitors in ectoderm lineage differentiation has been described. The SMAD pathway is described, for example, in Chambers et al, “Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling,” Nature Biotechnology, Vol. 27, No. 3, 2009. The NCC induction media may contain growth factors at various concentration and may be used for variable treatment times, the disclosed examples not intended to be limiting.

In one aspect, the HH signaling pathway activation may be carried out from about day 0 to about day 4 of the disclosed differentiation method. In a further aspect, the HH signaling pathway activation may be carried out from about day 0 to about day 10 of the differentiation method.

In one aspect, the activation may comprise contacting a precursor cell, such as an hPSC (pluripotent stem cell), with an HH agonist. HH agonists may be any small molecule or other agent capable of activating the HH signaling pathway, and identification of such agents will be readily understood by one of ordinary skill in the art. In one aspect, the HH agonist may be selected from a SMOOTHENED agonist (“SAG”), recombinant Shh (Sonic Hedgehog), Purmorphamine, or a combination thereof. In one aspect, the HH agonist may be selected from an antagonist that acts as a partial agonist at low dosage. For example, such HH agonists may be selected from Cyclopamine (1nM), and Vismodegib (GDC-0449), and combinations thereof.

In one aspect, the NCC obtained from the disclosed methods may be characterized by elevated expression of one or more of p75NTR, HNK1, RET, TFAP2B, SNAI1 SNAI2, SOX10 expression. The NCC may be characterized by expression of an enteric HOX code (such as, for example, HOXB3+, HOXB4+, HOXB5+).

In one aspect, the precursor cell may be a population of precursor cells, wherein the method provides a substantially homogenous population of neural crest cells that are primed to a neurogenic lineage. The posterior NC cells may, in some aspects, have elevated expression of neuronal progenitor markers (TUBB3), loss of SOX10 expression, and co-expression of an enteric HOX code (HOXB3+, HOXB4+, HOXB5+). In one aspect, the posterior NC cells are SOX10−, PHOX2B+, TUBB3high (Cluster 6 and 7); or TUBB3high, ELAVL4+ (Cluster 8). In a further aspect, the neural crest cell may be competent to make mature/functional neurons. The posterior NC cells, in a further aspect, may have reduced expression of NC markers (TFAP2A, SNAIL, SOX10) and elevated expression of neurogenic markers (TUBB3, ELVA4, PHOX2B).

In one aspect, the hPSC-derived NCC may be capable of giving rise to other non-neurogenic lineages, while activation of HH primes NCCs to the neurogenic lineage and make them more favorable toward the neuronal differentiation. In brief: in the absence of HH signaling activation, ENCCs are p75NTR+, HNK1+, RET+TFAP2A+, SNAIL+SOX10+ and express an enteric HOX code. With HH signaling activation, ENCCs (p75NTR+, HNK1+) are primed to the neurogenic lineage with reduced expression of NC markers (TFAP2A, SNAIL, SOX10) and elevated expression of neurogenic markers (TUBB3, ELVA4, PHOX2B). In one aspect, the ENCC cell is ENCC^(SAG0_10).

In one aspect, the HH agonist may be contacted with the precursor cell from about day 0 to about day 10 of the differentiation period, or from about day 0 to about day 4, or about day 4 to about day 10. In one aspect, the precursor cell is contacted with an HH activator (SAG) for a period of time sufficient to increase the number of SOX2+NANOG-cells

In one aspect, mature tissue (organoids) may comprise ENCCs (NC cells) differentiated into neurons. The mature tissue may be characterized by the formation of crypts and colonic epithelium and nerve cells, wherein the nerve cells are TUJ1+ neurons and S100b+ glia.

In one aspect, a method of making an innervated colonic organoid model is disclosed. In this aspect, the method may comprise the step of contacting an enteric NC cells (ENCCs) that is primed to neurogenic lineage using the methods disclosed herein, with a hindgut spheroid obtained from a precursor cell. The hindgut spheroid may be made by culturing gut tube spheroids in the presence of a BMP activator, and an EGF pathway activator (such as, for example, EGF); and transplanting the cultured hindgut spheroids with ENCCs that are primed to the neurogenic lineage into a kidney capsule of an immunodeficient host for a period of time sufficient for a mature tissue to form. In one aspect, the hindgut spheroid is derived from definitive endoderm, using methods known in the art.

In one aspect, the innervated organoid may be an innervated colonic organoid, wherein the innervated colonic organoid is characterized by expression of gut epithelium (CDH1+) and colon (SATB2+) markers was detected, and the presence of goblet (MUC2+)- and endocrine (GLP1+)-like cells.

In one aspect, an innervated HCO comprising hPSC-derived NC cells (ENCCs) and gut endodermal cells is disclosed. In one aspect, the innervated HCO may have a majority of neurons that are mature enteric neurons expressing Calretinin, Protein Gene Product 9.5 (PGP9.5+) and neurofilament (NFL+). In one aspect, the disclosed innervated HCO may comprise NCCs that are ENCC^(SAG0_10). In one aspect, the innervated HCO may comprise cells from two or more individuals or donors. In one aspect, the innervated HCO may comprise increased numbers of mature neurons (PGP9.5+, NFL+) as compared to an innervated HCO that is not treated with an HH agonist.

In one aspect, an NCC induction media composition is disclosed. The composition may comprise, for example, knockout Dulbecco's Modified Eagle Medium (“DMEM”) plus 15% Knockout Serum Replacement (“KSR) (about 0.1 to about 10 mM, or about 0.5 to about 5 mM, or about 1 mM, Life Technologies, 10828-028), NEAA (Life Technologies, 11140-050); L-glutamine (about 0.5 to about 10 mM, or about 1 to about 5 mM, or about 2 mM, Life Technologies, 25030-081); β-mercaptoethanol (55 μM, Life Technologies, 21985-023), and LDN193189 (100 nM, Stemgent) and SB431542 (10 μM, Tocris). Dual SMAD inhibitors and a potent GSK inhibitor may be added at different time frame during the NC induction, for example, LDN193189 (from day 0 to day 3), SB431542 (from day 0 to day 4). The composition may further include CHIR99021 (about 1 to about 15 μM, or about 2 to about 10 μM, or about 3 μM) (from day 2 to day 10, Tocris Bioscience, 4423). In one aspect, the composition may comprise retinoic acid.

Examples

The following non-limiting examples are provided to further illustrate embodiments of the invention disclosed herein. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent approaches that have been found to function well in the practice of the invention, and thus may be considered to constitute examples of modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes may be made in the specific embodiments that are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

In this study, Applicant applied single-cell RNA-Seq (scRNA-Seq) to establish differentiation trajectories directing human NC formation from hPSCs in vitro and identified that Hedgehog (HH) signaling is consistently activated in postmigratory NC-like cells. Profiling single-cell transcriptomes of NC and NC-derived neurons further revealed that activation of the HH pathway alters the topology of the neuronal differentiation path of NC and primes NC toward the neurogenic lineage. Applicant also found that the involvement of HH signaling in the transition from hPSCs to the NC lineage and the subsequent neuronal lineage differentiation were also directly illustrated using chemical- and gene-targeting-mediated modulation of HH signaling and in vitro models based on cells and newly established innervated HCOs.

Activation of the HH Pathway in Postmigratory NC-Like Cells

To generate heterogeneous populations of NC resembling various stages of in vivo development, unsynchronized hPSCs were used for differentiation. Posterior NC (HOX⁺) cells were generated using Applicant's previously established differentiation protocol (Lai et al., 2017). In brief, NC cells were derived from a control hPSC line using the stepwise differentiation protocol with dual-SMAD inhibitors, followed by caudalization with retinoic acid (RA) to obtain posterior NC cells. NC cells are then enriched by fluorescence-activated cell sorting (FACS) with HNK-1 and p75^(NTR) antibodies (FIG. 1A). Applicant quantified the transcriptional profiles of 392 FACS-enriched hPSC-derived NC cells. Applicant then used t-distributed stochastic neighbor embedding (t-SNE) to visualize gene expression dynamics during the hPSC-to-NC transition at the single-cell level. t-SNE mapped the expression profiles of individual cells within the FACS-enriched hPSC-NC pool on a two-dimensional t-SNE space and placed cells with similar expression profiles in proximity to each other. Due to asynchrony in differentiation, five distinct cell populations were identified from the hPSC-derived NC pool (FIG. 1B, left panel). Applicant computed a proliferation index based on an unsupervised selection of cell-cycle-associated genes to estimate the relative proliferative rates of these clusters. Applicant found that clusters 1 and 2 represented the most proliferative groups of cells in the pool (FIG. 1B, right panel). During early NC induction, unique sets of transcription factors were expressed to mediate the formation of NC at the neural plate border, NC specification, and the subsequent delamination and migration of the NC cells (FIG. 1C). To reveal the identity of the identified clusters, Applicant examined the expression of several well-characterized NC markers—neural plate border specifiers (MSX1, MSX2, PAX3, PAX7, ZIC1), NC specifiers (TFAP2B, SNAI1 SNAI2, SOX9, SOX10), postmigratory NC (FOXD3) and neuronal progenitor (TUBB3) markers—in these 5 clusters of cells (FIG. 1D). With cross-referencing to the proliferative indexes of these clusters, Cluster 1 expressed a gene set resembling NC cells (FOXD3⁻, ZIC1⁺) residing at the neural plate border before delamination and with the highest proliferative rate, representing the less mature NC cells. Clusters 2, 3 and 4, on the other hand, resembled postmigratory vagal NC cells (FOXD3⁺, PHOX2B⁺, HOXB3⁺, HOXB5⁺). Notably, RUNX2 and PHOX2B were co-expressed in these three clusters, suggesting that these cells are capable of differentiation toward neurogenic and skeletogenic lineages. Unlike Clusters 2 and 4, Cluster 3 also expressed ISL1 and the position codes similar to cardiac (HOXA2⁺, HOXA⁺, HOXB2⁺, HOXB3⁺, HOXC4⁺, HOXD3⁺) NC cells (FIG. 1E). Cluster 5 was predicted to be more committed NC cells; they were least proliferative and possessed neuron-like features, including an elevated expression of neuronal progenitor marker (TUBB3), accompanied by the loss of RUNX3 and SOX10 expression, and coexpression of an enteric HOX code (HOXB3⁺, HOXB4⁺, HOXB5⁺). In summary, Applicant identified five transitional states in a pool of NC cells derived from hPSCs, in which the majority of the NC intermediates possessed differentiation plasticity toward both the neurogenic and skeletogenic lineages, and their proliferation capacities were inversely correlated to their differentiation status (FIG. 1F).

Applicant anticipated that the overall yield of functional NC cells may be improved by dictating the less mature NC intermediate (Cluster 1) to the more mature states, similar to those postmigratory NC-like cells (Clusters 2, 3 and 4) or the neuron-like cells (Cluster 5). A recent single-cell transcriptome study revealed that Sonic hedgehog (Shh) is upregulated in NC cells at the migratory front during chick development (Morrison et al., 2017) and influences the migratory path of NC cells (Testaz et al., 2001). There is also increasing evidence to show that HH signaling activity determines the early lineage fate decisions and the lineage transition of hPSC toward mesoderm (McIntyre et al., 2013) and ectoderm lineages (Calder et al., 2015). Therefore, Applicant examined the expression of HH target genes in these 5 NC intermediates to estimate the possible involvement of HH signaling during the hPSC-to-NC transition. Consistently, Applicant found that the expression of a GLI activator (GLI2) and its direct target gene (PTCH1) are elevated in cells most competent for migration and neurogenic lineage differentiation (Clusters, 2, 3 & 4), but they were not expressed in the immature NC (Cluster 1) or the neuron-like cells (Cluster 5) (FIG. 1G). This result may imply that transient modulation of HH signaling during NC induction may promote the formation or enrichment of these postmigratory NC-like cells and improve the overall yield of functional NC cells. GLI3, on the other hand, was expressed in all five of these clusters at similar expression levels and may not be actively involved in this process.

Level of HH Signaling Determines NC Yield from hPSCs

Single-cell transcriptome analysis showed that HH signaling is transiently activated in post-migratory NC-like cells. Here, Applicant performed independent experiments to further address how HH signaling may affect the hPSC-to-NC transition. Applicant employed a pharmacological approach to manipulate HH signaling at the early and late phases of in vitro differentiation. A well-known agonist and antagonist of SMOOTHENED (SAG and cyclopamine, respectively) were added for various time frames during in vitro differentiation to activate and suppress HH signaling, respectively (FIG. 2A & 2D). The addition of SAG in the differentiation medium during the whole differentiation process (days 0-10, constant) significantly increased the yield of HNK-1⁺p75^(NTR+) cells as detected by flow cytometry (19.6±0.51% in the untreated group versus 42.5±9.3% in the group with constant SAG treatment). Intriguingly, the SAG treatment time could be shortened to as little as 4 days. If SAG was added for 4 days in the early phase of the in vitro differentiation (day 0-4), up to 44.6±9.1% of cells were HNK-1 and p75^(NTR) double positive, and the NC yield was highly comparable to that in the 10-day treatment group (FIG. 2B & 2C). Conversely, the addition of cyclopamine during the early phase of the in vitro differentiation dramatically suppressed the hPSC-to-NC transition, as evidenced by the reduced percentage of HNK-1⁺p75^(NTR+) cells (FIGS. 2E & 2F). In addition, when Applicant suppressed HH signaling by constitutively expressing the repressor form of GLI3 in hPSCs (GLI3^(Δ699/Δ699)), the percentage of HNK-1⁺p75^(NTR+) cells was dramatically reduced. The results indicated that the proper level of HH signaling impacts the early phase of the hPSC-to-NC transition. A high level of HH signaling at the early phase of the in vitro differentiation favors the hPSC-to-NC transition and promotes the generation of HNK-1⁺p75^(NTR+) NC-like cells, while constitutive suppression of HH signal abrogates this process.

The level of HH signaling regulates the expression of cell patterning and neurogenesis mediators during the hPSC-to-NC transition

Applicant's data show that SAG treatment enables efficient NC derivation from hPSC and improves the NC yield from hPSC. HH serves as a patterning factor in central nervous system (CNS) lineage differentiation, and HH has been shown to promote spinal cord motor neuron (pMN) derivation from hPSCs (Calder et al., 2015). Therefore, Applicant analyzed the transcriptomes of hPSC-derived NC cells using bulk RNA sequencing to examine whether activation of HH signaling alters their biological nature. Spearman correlation analysis was performed to estimate the correlation of the overall gene expression profiles between 3 human fibroblast (hFib) lines, 3 human pluripotent stem cell (hPSC) lines, NC cells derived from 2 hPSC lines in the absence (NC) or in the presence (NC^(SAG0-10)) of SAG, NC derived from a GLI3 mutant hPSC (NC^(GLI3Δ699/Δ699)) line, neuronal derivatives of hPSC-NC (hPSC-PNS neurons), and CNS progenitors derived from 1 hPSC (hPSC-CNS progenitor) line and their neuronal derivatives (hPSC-CNS neurons) in replicates. Transcriptomic data for CNS progenitors and their neuronal derivatives were obtained from public databases (ENCODE ref: ENCSR244ISQ and ENCSR023VVO). As expected, correlations were highest between cells at similar cellular stages, so Applicant considered them replicates of hypothetical cellular stages as indicated in FIG. 3A. Intriguingly, strong correlations were also observed between NC^(SAG 0-10), NC^(GLI3Δ699/Δ699) and hPSC-NC, suggesting that NC^(SAG0-10) and NC^(GLI3Δ699/Δ699) likely retain their NC nature.

From the bulk RNA sequencing data, Applicant identified 2,850 differentially expressed genes (DEGs) in NC^(SAG0-10) cells, including 1,817 upregulated and 1,033 downregulated genes, while 1,740 and 839 genes were up- and downregulated in NC^(GLI3Δ699/Δ699) cells in comparison with the control (hPSC-NC) (log₂ fold change≤1.5; adjusted p<0.05). Interestingly, 461 and 421 genes were consistently up- and downregulated, respectively, in both NC^(SAG0-10) and NC^(GLI3Δ699/Δ699) (FIG. 3B). Gene Ontology (GO) enrichment analysis showed enrichment of patterning and neural GO terms in both NC^(SAG0-10) and NC^(GLI3Δ699/Δ699) (FIG. 3C & 3D), suggesting that an appropriate level of HH signaling is required in these biological processes. Unlike in NC^(SAG0-10) cells, cell death signaling (response to tumor necrosis factor) was elevated in NC^(GLI3Δ699/Δ699) (FIG. 3D), implying that NC^(GLI3Δ699/Δ699) may have poor survival. A volcano plot was generated using DEGs identified in NC^(SAG0-10) and NC^(GLI3Δ699/Δ699) (FIG. 3E). Applicant found that genes involved in patterning were consistently downregulated when HH signaling was elevated or suppressed, while transcription factors regulating neurogenesis (OTX1, OTX2, NKX6-1) were consistently upregulated in NC^(SAG0-10) and NC^(GLI3Δ699/Δ699). On the other hand, the expression levels of neural plate specifiers (ZIC1, PAX3) were elevated only in NC^(GLI3Δ699/Δ699), while SAG treatment upregulated the expression of ITGB genes accompanied by downregulation of CLDN, which favors NC migration. The results indicate that activation of HH signaling may increase not only the yield of NC cells from hPSCs but also their neurogenic potency.

SAG Treatment Primes NC Toward the Neurogenic Lineage

To understand how HH signaling influences the topology of the neuronal differentiation path of NC, Applicant profiled additional 1,146 single-cell transcriptomes of NC cells with the constant (day 0-10) or early-phase (day 0-4) SAG treatment and NC-derived neurons sampled from day 32 of differentiation as shown in FIG. 4A. Together with 392 control NC cells, a total of 1,538 individual cells were sequenced with 5844 median genes and 1.16 million mean confident mapped reads per cell (FIG. 8). Applicant then projected all single cells on the principal component analysis (PCA) plots to visualize the heterogeneity of gene expression profiles and find subpopulations that emerge upon the SAG treatments and during differentiation. Eight major transcriptionally distinct clusters were identified in NC, NC^(SAG0-4), NC^(SAG0-10) and neurons, including 2 clusters (Clusters 6 & 7) that were present only in the SAG treatment groups (FIG. 4B). Applicant then further built a k-nearest-neighbor graph over cells in high-dimensional gene expression space and generated an interactive 2D visualization of the cell graph using SPRING. This representation revealed that the NC differentiation trajectory during early neural commitment consists of eight apparent states (FIG. 4C). The differentiation trajectory began with the NC (control) with the five NC intermediates inferred using t-SNE (FIG. 1), the less mature NC (Cluster 1) to the postmigratory NC intermediates (Cluster 2, 3 & 4), passing through the neuron-like cells (Cluster 5), and terminated at a mature neuron state (TUBB3^(high), ELAVL4⁺) (Cluster 8). Two additional NC intermediates (SOX10⁻, PHOX2B⁺, TUBB3^(high)) were identified in the SAG treatment groups (Clusters 6 & 7), representing up to 75% of the total population (FIGS. 4C, D, & F). Clusters 1 and 6 were most proliferative, while the less mature NC intermediates (Cluster 1-4) were more migratory (FIG. 4E). As shown in FIG. 4F, the populations of the less mature NC intermediates (Clusters 1-4) were gradually reduced and replenished by the neuron-like cells (Clusters 5-7) upon the SAG treatments (NC^(SAG0-4) & NC^(SAG0-10)), and this effect was more profound in the constant SAG treatment group (NC^(SAG0-10)). These data suggest that the SAG treatment primes NC toward the neurogenic lineage and favors the NC-to-neuron transition.

Applicant further analyzed the molecular dynamics during the NC-to-neuron transition in the presence or absence of SAG. Applicant divided the cells into three classes corresponding to the three major developmental stages inferred by the pseudotime analysis: early (Stage 1), intermediate (Stage 2) and late (Stage 3) and analyzed the sequential changes of all DEGs during the stage transitions (FIG. 9). Genes in Clusters 1-4 gradually downregulated from the beginning of the differentiation trajectory were largely involved in “neural crest differentiation/development” and “PI3K-Akt signaling” and “ECM”-receptor interaction. A subset of genes in Cluster 5 was gradually upregulated in Stage 2, and they were strongly enriched for GO terms “cell fate commitment”, “Notch signaling pathway” and “autonomic nervous system development”, while the genes upregulated during the transition to the final stage were mainly enriched for “axon development” (FIG. 4G & 10).

Compared with the control group, SAG treatment transiently upregulated a subset of Cluster 5-specific genes and induced a temporary transcriptional wave (FIGS. 4G & 11). It is noteworthy that the two SAG-specific NC intermediates (Clusters 6 & 7) emerged during the Stage 1-to-Stage 2 transition and exhibited unique gene expression profiles with predominant involvement in the GO terms “metabolism-related pathways” (FIG. 12). On the other hand, SAG treatment did not induce any temporary transcriptional wave at Stages 1 & 3, but it may accelerate NC differentiation by downregulating the NC-specific genes (FIG. 4G). Applicant then focused on transcription factors (TFs) differentially expressed in progressive cell fate transition from NC to neuron and constructed the gene network based on their pairwise correlations. Three subnetworks were revealed chronologically, in which most of Stage 2 and some of Stage 3 TFs were upregulated by SAG treatment (yellow circles, FIG. 4H). More importantly, the Stage 2 subnetwork connected with genes in Stage 3, suggesting that the SAG treatment activates the transcriptional circuits for initiating cell commitment/differentiation, priming NC toward the neurogenic lineage.

SAG-NC Cells Exhibit Better Differentiation Competency to Generate Dopaminergic (TH+) and Cholinergic (VIP+) Neurons

Applicant's bulk- and single-cell RNA sequencing data indicate that NC^(SAG0-10) cells retain the NC nature with enhanced neurogenic potency. For instance, the dopaminergic neuron differentiation pathway was found to be upregulated concomitant with activation of HH signaling. Thus, Applicant further examined whether SAG treatment during the hPSC-to-NC transition would provide NC cells with better differentiation competency to form various subtypes of neurons. Control, NC^(SAG0-10) and NC^(GLI3Δ699/Δ699) cells were generated, FACS-enriched and directed to neurogenic lineage differentiation as shown in FIG. 5A. Consistent with the transcriptomic data, most of the NC^(SAG0-10) and NC^(GLI3Δ699/Δ699) cells expressed a lineage marker for NC (SOX10) but not for CNS (PAX6) (exemplary data in FIG. 5B). Unlike the control NC and NC^(SAG0-10) cells, Applicant found that many of the NC^(GLI3Δ699/Δ699) cells underwent spontaneous differentiation toward the neurogenic lineage, showing the expression of pan-neuronal markers (e.g., HU, TUJ1) even in the absence of neuronal differentiation induction (FIG. 5C). These immature neuronal cells eventually died within a few days, which would be the result of the upregulation of the cell death pathway as indicated in the transcriptomic data.

On the other hand, NC^(SAG0-10) cells could grow and expand as competently as the control cells. Applicant then examined the differentiation potential of NC^(SAG0-10) cells on the basis of their neuronal differentiation capability, as monitored by the expression of pan-neuronal markers (HU, TUJ1 and PGP9.5) and subtype markers, such as tyrosine hydroxylase (TH) for dopaminergic neurons and vasoactive intestinal polypeptide (VIP) for cholinergic neurons, which are the major subtypes of nerve cells found in the ENS. As shown in FIG. 5D, the NC and NC^(SAG0-10) cells could give rise to comparable numbers of neurons expressing various pan-neuronal makers. Importantly, NC^(SAG0-10) cells exhibited better differentiation competency and required a shorter differentiation time to generate TH⁺ and VIP⁺ neurons. Significantly greater numbers of TH⁺ and VIP⁺ neurons were obtained from NC^(SAG0-10) cells at day 22 of differentiation when compared to the control (FIG. 5D). In the control group, numbers of TH⁺ and VIP⁺ neurons comparable to those in the SAG treatment group at day 22 were observed only on day 30 of differentiation as described previously (Lai et al., 2017).

Establishment of an Innervated Colonic Organoid Model Comprising Functional Neurons

Applicant established an innervated HCO model for appraising the functional competency of hPSC-derived NC cells. Hereafter, the NC cells used for the generation of the innervated HCOs will be termed ENCCs. In brief, the disclosed organoid model may comprise two major components: ENCCs and gut endodermal cells. As shown in FIG. 6A, the ACTIVIN-NODAL and WNT pathways were activated sequentially to promote the formation of definitive endoderm and hindgut spheroids, respectively. On day 6, hPSCs had differentiated into definitive endoderm coexpressing SOX17 and FOXA2 (FIG. 6B). The free-floating spheroids derived from the definitive endoderm were collected on days 8-10 and cultured with the FACS-sorted ENCCs in three-dimensional (3D) Matrigel, in which ENCCs received patterning signals from the gut endoderm and developed together with the endodermal cells. The hindgut spheroids were then caudalized further by the addition of BMP2 (FIG. 6A). By 28 days, the HCOs showed villus-like structures containing a distinct layer of gut epithelium (VILLIN⁺, CDH1⁺) expressing a colon-specific marker (CA4⁺) and goblet cells (MUC2⁺) (FIG. 6C). Intriguingly, ENCCs showed the ability to self-pattern, align with the epithelium, and start differentiating into neurons (TUJ1⁺) (FIG. 6C). After transplantation into the kidney capsule of immunodeficient mice, HCOs underwent morphogenesis and formed mature tissues with defined crypts and colonic epithelium, while ENCCs gave rise to nerve cells (TUJ1⁺ neurons and S100b⁺glia) residing near the submucosal and myenteric layers of smooth muscle fibers (FIG. 5D). Consistently, expression of gut epithelium (CDH1⁺) and colon (SATB2⁺) markers was detected, and goblet (MUC2⁺)- and endocrine (GLP1⁺)-like cells were found in the mature HCOs (FIG. 5D).

The nerve cells in the innervated HCOs were functional. Muscular contractions were observed when the explanted kidney grafts were subjected to low-voltage electrical-field stimulation (EFS). As shown in FIG. 6E, HCO tissue without ENCCs was subjected to two 5-ms pulses at 30 V with a 30-second interval, which caused a single contraction immediately after each pulse, suggesting the direct stimulation of smooth muscle (FIG. 6E, upper left panel). In contrast, in the HCO+ENCC group, two 5-ms pulses at 30 V were sufficient to trigger a sustained wave of contractions (FIG. 6E, lower left panel). To determine whether the contractions were a result of the activity of the nerve cells, Applicant blocked neuronal activity with tetrodotoxin (TTX), which binds to voltage-gated Na⁺ channels on nerves, thereby inhibiting the firing of action potentials. TTX completely inhibited the EFS-induced contractions (FIG. 6E, lower right panels). In summary, the innervated HCO represents a useful human model for testing the functional competency of enteric neurons.

Early Activation of HH Improves the Functional Competency of ENCC-Derived Neurons as Revealed by the Innervated HCO Model

Applicant then examined the impact of SAG treatment on the function of ENCC-derived neurons on the basis of inducing HCO contractions. Innervated HCOs were generated using ENCCs^(SAG0_10). Consistently, Applicant found that ENCCs^(SAG0_10) grew better than the control ENCCs with HCOs in vitro, and more TUJ1⁺ and TH⁺ cells were found aligned with the epithelial cells of HCOs in the SAG treatment group (FIG. 7A). The HCO+ENCCs^(SAG0_10) explants contained crypts and colonic epithelium, highly comparable to that of the control group (FIG. 7B). Intriguingly, more mature neurons expressing Protein Gene Product 9.5 (PGP9.5) and neurofilament (NF) were detected in the SAG treatment group, while the majority of neurons detected in the control group expressed only the neuronal progenitor marker TUJ1. On the other hand, CALRETININ-positive nerve cells were detected in all innervated HCO explants (HCO+ENCCs and HCO+ENCC^(SAG0_10)), suggesting that most NC-derived neurons are excitatory neurons (FIG. 7C). Regarding the functional competency of the neurons, the explanted kidney grafts from the HCO+ENCC^(SAG0_10) group consistently exhibited a more profound series of wave-like contractions. The contractions were more dramatic and sustainable when compared to the HCO+ENCC group (FIG. 7D, left panel). Consistently, TTX completely inhibited the ability of low-voltage stimulation to trigger contractile activity in explanted kidney grafts (FIG. 7D, right panel). Taken together, the data suggest that neurons derived from ENCC^(SAG0_10) exhibit better functional competency.

To further examine the neuromuscular coupling mediated by the ENCC-derived neurons, Applicant randomly dissected part of the HCO explants from each group for functional tests. Applicant activated the ENCC-derived neurons using the selective α3-nicotinic receptor agonist dimethylphenylpiperazinium (DMPP), which increases nerve excitability by inhibiting Na+ channel inactivation. As illustrated in FIG. 7E, DMPP induced muscle contraction in HCOs+ENCCs, while no contraction was observed with HCOs alone. Muscle contraction was mediated by ENCC-derived neurons because the addition of TTX completely abolished muscle contraction. In addition, stronger contractile responses were usually observed in the SAG-treated group (HCO+ENCC^(SAG0_10), FIG. 7E). This observation was reproducible across independent experiments and innervated HCOs derived from two different hPSC lines (FIG. 7F).

Discussion

Lineage decision making is fundamentally a single-cell process, and the response to lineage-specifying signals depends on the state of the individual cell. Therefore, directed differentiation of hPSC usually gives rise to heterogeneous populations, resembling cells at various intermediate differentiation states during development in vivo. High-resolution RNA sequencing of hPSC derivatives allows us to identify the unique expression profiles of these intermediate populations and estimate their migration and proliferation capacity. By cross-referencing the stage- and cell-fate-specific markers gleaned from the in vivo studies, the stereotypical sequence of these intermediate states and the differentiation trajectories directing human NC formation from hPSCs can be established. In addition, the sequential molecular dynamics that direct NC toward the neurogenic lineage can be depicted by building the pseudotime trend for the NC-to-neuron transition, such that the ordered activation of transcriptional waves throughout the trajectory of neuronal differentiation can be revealed. A better understanding of the decision-making process that underlies cell fate progression will help improve the existing differentiation protocol in a systematic way.

Applicant's scRNA-Seq analysis revealed five subpopulations from the hPSC-derived NC pool, and each subpopulation of cells possesses a distinctive expression profile and a different proliferation and migration capacity. They resemble the premigratory NC cells at neural plate border or the postmigratory NC with unique HOX codes and differentiation potentials toward neurogenic and skeletogenic lineages. Given that only approximately 20% of cells belong to the border-like cells of the neural plate (the immature NC), Applicant considered that the differentiation protocol is robust for directing NC differentiation of hPSCs. Among these 5 clusters, cells in Cluster 1 were most proliferative, but they were immature and less committed. The postmigratory NC-like cells (Clusters 2, 3 and 4), on the other hand, should have been poised for neurogenic and skeletogenic lineage differentiation, and cells in Cluster 5 were most mature and they were committed to the neurogenic lineage with elevated expression of the early neuronal markers. Applicant may therefore improve the overall differentiation potential of the hPSC-derived NC pool by eliminating Cluster 1 or by directing them to differentiate forward and become postmigratory NC- or neuron-like cells. HH signaling is activated solely in the 3 subpopulations of postmigratory NC-like cells, while it is inactive in the immature NC- and committed neuron-like cells, suggesting that transiently modulating the level of HH signaling during the hPSC-to-NC transition may improve the NC yield and/or their capability of differentiating into neurogenic lineages.

To determine an appropriate HH signaling level and the treatment window favorable for deriving NC, Applicant used SAG and cyclopamine to activate and inhibit HH signaling, respectively, throughout the hPSC-to-NC transition process or only during the early or late phase. Surprisingly, the HH signaling level during the early phase of the hPSC-to-NC transition was found to determine the NC yield. The validation experiments indicated that a brief activation of HH pathway during the early phase of NC induction significantly enhances the ectoderm lineage commitment of hPSC and increases the number of SOX2⁺NANOG⁻ cells at day 4 of differentiation (FIG. 13). A longer SAG treatment (4 days) further induced the formation of NC, and NC-like cells (SNAIL⁺) emerged as early as day 4 of differentiation when SAG was added to the differentiation cocktail (FIG. 14). Nevertheless, prolonged (day 0-10) or late-phase (day 4-10) SAG treatment indeed boosted the NC-to-neuron transition (FIG. 15). The subsequent molecular dynamics and network analyses suggest that at least three subsets of gene regulatory circuits are involved in mediating the NC-to-neuron transition, where the Stage 2 and Stage 3 subnetworks are interconnected. SAG treatment, in particular, robustly upregulated the key TFs implicated in these two interconnecting subnetworks, implying that the activation of the HH pathway likely favors the Stage 2-Stage 3 transition and primes NC toward the neurogenic lineage (FIGS. 4G & 4H). In concordance with this observation, two unique populations of NC intermediates (Clusters 6 & 7) representing up to 75% of the total population emerged upon the SAG treatment, and these cells had acquired some neuron-like cell features, sharing similar molecular signatures with the cells in Cluster 5. Furthermore, NC^(SAG0-10) consistently could give rise to more mature enteric neurons and of better functional competency, as illustrated in the disclosed in vitro cell and the innervated HCO models. Given that metabolic pathways were robustly activated in these two clusters of cells, it is conceivable that the enhanced cellular metabolism functions as a booster in the NC-to-neuron transition, particularly favoring neurogenesis.

In this study, Applicant also established a new differentiation protocol for generating innervated HCOs and used it for assessing the functional competency of the hPSC-derived NC cells. It is a near-physiological model, in which NC cells lined up along the epithelial cells of HCOs, self-organized and gave rise to the enteric neurons in response to the inductive cues from the developing HCOs, recapitulating the gut morphogenesis process in vivo. Consistent with Applicant's in vitro data, the HCO explants from the SAG treatment group contained more mature enteric neurons (PGP9.5⁺ and NFL⁺) than the control group. More importantly, Applicant found that the SAG treatment greatly improves the survival and engraftment efficiency of the ENCCs to HCOs and strengthens the contractile responses of the innervated HCOs, in results that are highly reproducible among independent experiments as well as across different hPSC lines.

In summary, Applicant has established an experimental algorithm that provides guidance for more efficient ways to generate mature neurons from hPSC-derived NC. The scRNA-Seq analysis revealed that HH signaling represents the differentiation cue associated with the transition from immature NC intermediates to more mature postmigratory NC-like cells and the priming of NC toward the neuronal lineage. Windows of opportunity have been identified at the early and late phases of the hPSC-to-NC transition, which can be exploited to guide NC lineage differentiation with maximal yield and functional competency, respectively. More importantly, the disclosed innervated HCO model represents an in vitro system closely resembling how a real gut functions and has the potential to drive breakthroughs not only in mechanistic studies of various gastrointestinal diseases but also in drug development and toxicity tests.

Derivation of Neural Crest (NC) from hPSC Lines

At day 0, Control or mutant hiPSCs were seeded on Matrigel-coated plate (105 cells cm-2) in iPS cell medium containing 10 ng ml-1 FGF2 (PeproTech, 100-18B) and 10 μM Y-27632. Differentiation was then initiated by replacing iPS cell medium with KSR medium, containing knockout DMEM plus 15% KSR (Life Technologies, 10828-028), NEAA (Life Technologies, 11140-050), L-glutamine (Life Technologies, 25030-081), β-mercaptoethanol (Life Technologies, 21985-023), LDN193189 (100 nM, Stemgent) and SB431542 (10 μM, Tocris). The dual SMAD inhibitors and a potent GSK inhibitor were added at different time frame during the NC induction, including LDN193189 (from day 0 to day 3), SB431542 (from day 0 to day 4), 3 μM CHIR99021 (from day 2 to day 10, Tocris Bioscience, 4423). The NC cells were finally caudalized with 1 μM retinoic acid (from day 6 to day 9). The KSR medium was gradually changed to N2 medium at day 4 by increasing N2 from 25% to 75% from day 4 to 9 as described previously (Lai et al., 2017). The N2 medium contained neural basal medium (Life Technologies, 22103-049) and DMEM/F12 (Life Technologies, 10565-018 (1:1), N2 supplement (Life Technologies, 17502-048), B27 supplement (Life Technologies, 17504-044) and insulin (Life Technologies, 12585-014). SAG (1 μM, Sigma, SML1314) was added (day 0-10) during the in vitro differentiation. The NC cells were enriched by FACS with antibodies against p75NTR and HNK-1 at day 10 of the differentiation as described (Fattahi et al., 2016; Lee et al., 2010; Lee et al., 2007; Zeltner et al., 2014).

For cell sorting, HNK-1/p75NTR stained cells were washed and resuspended in PBS with 2% FBS. The HNK-1 and p75NTR double positive cells were enriched using fluorescence activated cell sorting (FACS) (BD FACSAria III Cell Sorter). The HNK-1 and p75NTR double positive cells were gated and sorted using the four-way purity mode and the purity of sorted cells was >96% and evaluated by flow cytometry. The sorted neural crest cells were collected for immunostaining or subsequent experiments.

Derivation of HCOs from hPSCs

Cells were fed mTeSR1 media and routinely passaged using Dispase II (Gibco). NC cells were generated as described above, and HCOs were generated according to a published protocol (Munera et al., 2017). NC and HCOs were then combined at an early stage of colon differentiation to generate HCOs containing nerve cells (FIG. 6A). Briefly, for induction of definitive endoderm (DE), hPSC were passaged with Accutase (Invitrogen) and plated at a density of 100,000 cells per well in a Matrigel-coated, Nunclon surface 24-well plate. For Accutase-split cells, 10 μM Y-27632 compound (Sigma) was added to the media for the first day. After the first day, the medium was changed to mTeSR1, and cells were grown for an additional 24 hr. Cells were treated with 100 ng/mL of Activin A for 3 days, and DE was then cultured in hindgut induction medium (RPMI 1640, 2 mM L-glutamine, 2% decomplemented FBS and penicillin-streptomycin) for 4 days with 500 ng/mL FGF4 (R&D) and 2 μM CHIR99021 (Tocris) to induce formation of mid-hindgut spheroids. Spheroids were collected from 24-well plates, pooled, mixed with 5,000 FACS-sorted NC cells, and plated in Matrigel (BD) at a minimum of 30 spheroids per well. To generate HCOs, spheroids were overlaid with 100 ng/mL EGF plus 100 ng/mL BMP2 (R&D) for 3 days. The medium was then changed twice weekly thereafter. HCOs were re-plated in fresh Matrigel every 5-7 days at a density of 5⁻¹⁰ organoids per well. Cultures were fed a basic gut medium (advanced DMEM/F12, 1×B27 supplement, 1×N2 supplement, 10 μM HEPES, 2 mM 1-glutamine, 1×Pen-Strep) supplemented with 100 ng EGF ml⁻¹ and maintained in vitro for up to 8 weeks.

In vivo transplantation, electrical-field stimulation and ex vivo neuromuscular coupling test of HCOs

HCOs+ENCCs were ectopically transplanted into the kidney capsule of NOD/SCID mice following a previously developed protocol(Workman et al., 2017). Briefly, 5-8-week-old HCOs were embedded in collagen and transplanted into the kidney subcapsular space. Engrafted HCOs were harvested 8-10 weeks after transplantation and either analyzed for neural and glial markers or used for electrical-field stimulation (EFS) experiments and ex vivo neuromuscular coupling tests. For EFS, HCOs, HCOs+ENCCs and HCOs+SAG-ENCCs were explanted into Tyrode's solution and equilibrated for approximately 5 min before stimulation was begun. Electric stimulation was applied using a Grass S88 Stimulator (Grass Technologies) with 2-3 pulses, 5-ms duration and 30 V settings. HCO, HCOs+ENCCs and HCOs+SAG-ENCCs were then incubated for 5 min in 10 μM Tetrodotoxin (TTX) diluted in Tyrode's, rinsed and placed back in fresh Tyrode's. EFS was then repeated. Videos were recorded on a Leica dissection microscope using Leica Application Suite software and processed with VideoLAN and Handbrake to achieve 16× play speed. Videos were analyzed using the video-analysis software Tracker version 4.91 (Douglas Brown). Automated point tracking with position was performed to measure the movement within explanted HCOs, HCOs+ENCCs and HCOs+SAG-ENCCs during EFS.

For ex vivo neuromuscular coupling test, engrafted HCOs, HCOs+ENCCs and HCOs+SAG-ENCCs were harvested and placed in ice-cold HBSS. Muscle strips (4-6 mm in length and 1-2 mm in width) were cut from the engrafted HCOs, HCOs+ENCCs and HCOs+SAG-ENCCs. Preparations were suspended isometric-force organ-bath chambers filled with Krebs solution (117 mM NaCl; 4.7 mM KCl; 1.2 mM MgCl2; 1.2 mM NaH2PO4; 25 mM NaHCO3; 2.5 mM CaCl2, and 11 mM glucose), warmed at 37° C. and with 95% O₂+5% CO₂. After an equilibration period of 60 min, the contractile response of the muscle was continuously recorded, using a four-chamber tissue-organ bath with isometric-force transducers (AD Instruments) coupled to a computer equipped with LabChart Pro software (AD Instruments). Muscle preparations were stimulated with dimethylphenylpiperazinium (DMPP; 10 μM; Sigma-Aldrich). Chemical stimulations were applied at 15-min intervals and followed by three washes. TTX (10 μM) was applied 5 min before DMPP stimulation. The effects of chemical stimulation on tension were evaluated by measuring the area under the curve (AUC). Data are expressed in ΔAUC, i.e., “stimulated” AUC measured 120 s after stimulation minus “control” AUC measured 120 s before stimulation.

Human Induced Pluripotent Stem Cells (hiPSC)

A control hiPSC line (IMR90-iPSC) was obtained from WiCell Research Resources (Wicell, WI., RRID:CVCL C434). Another control hiPSC cell line (UE023023) was generated from urine derived cells of a male individual by episomal reprogramming vectors carrying the four reprogramming factors(Xue et al., 2013). All iPSCs used in this study were at the intermediate (35-65) passage numbers and maintained on matrigel (BD Biosciences, 354234)-coated plate with mTeSR1 medium (StemCell Technologies, 05850).

Generation of the GLI3 Mutant hPSC Line

The CRISPR/Cas9D10A system (Mali et al., 2013) was used to target Exon 13 of the GLI3 gene in IMR90-iPSCs. A pair of guide RNAs (gRNAs) targeting GLI3 were cloned into a gRNA expression vector (Addgene, 41824) using Gibson assembly. Four million of IMR90 iPSCs were transfected with gRNA constructs and the human codon-optimized Cas9D10A expression plasmid (Addgene, 44720) by electroporation using Nuclofector transfection kit (Lonza, VPH-5022). After transfection, the cells were seeded on Matrigel-coated plate with mTeSR1 medium for 48 hours, and then GFP-expressing cells were sorted into Matrigel-coated 96-well plate by FACS to get single cell. Single colony was formed around 7-14 days and then the single colony was passaged twice using ReLeSR™ (StemCell Technologies, 05872). Subsequently, the genomic DNA was isolated and the targeted region of GLI3 gene was PCR amplified using primers: Sanger sequencing was performed using the PCR products after treated with exonuclease I and shrimp alkaline phosphatase. The hPSC clones with bi-allelic nonsense mutations were expanded for follow-up assays.

FACS and Flow Cytometric Analysis

For flow cytometry analysis, the 10 day-differentiated cells were dissociated with Accutase and then incubated with anti-human antibodies including APC-HNK-1 (BD Pharmingen, 560845) and FITC-p75^(NTR) (Miltenyi Biotec, 130-091-917) for 30-45 minutes on ice. To stain for PE-RET (Neuromics, FC15018), the cells were fixed in 4% paraformaldehyde for 10 minutes at room temperature and permeabilized using 0.1% (w/v) Saponin solution, then washed and blocked in PBS with 2% FBS. The cells are then stained with antibodies for 30-45 minutes on ice. Approximately 10⁶ cells were stained and labeled cells were detected using a FACSAriaIII (Becton Dickinson Immunocytometry Systems, San Jose, Calif., USA). Isotype-matched antibodies were used as controls. FlowJo version 8.2 (Tree Star, Inc.) was used to analyze flow data.

For cell sorting, HNK-1/p75^(NTR) stained cells were washed and resuspended in PBS with 2% FBS. The HNK-1 and p75^(NTR) double positive cells were enriched using fluorescence activated cell sorting (FACS) (BD FACSAria III Cell Sorter). The HNK-1 and p75^(NTR) double positive cells were gated and sorted using the four-way purity mode and the purity of sorted cells was >96% and evaluated by flow cytometry. The sorted neural crest cells were collected for immunostaining or subsequent experiments.

Immunoblotting

To examine the expression levels of the activator and repressor forms of GLI3 in the control and GLI3^(Δ699/Δ699)-hiPSC-derived NC cells, NC cells were derived from the control and GLI3 mutant hiPSC lines and enriched by FACS as described above. FACS-sorted NC cells were then expanded in culture with N2 medium containing 10 ng/ml FGF2, 3 μM CHIR99021 and 10 μM Y-27632 for one week. Cells from two wells of 12-well plate were collected and then lysed with cell lysis buffer containing 20 mM Tris (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 2.5 mM sodium pyrophosphate, 1 mM β-glycerophosphate, 1 mM Na₃VO₄, 1 μg/mL leupeptin and 1 mM phenylmethanesulfonyl fluoride (PMSF). Cell lysates containing 60 μg of total protein were separated on 8-12% SDS-polyacrylamide gels and blotted onto nitrocellulose membranes. The membranes were then incubated with goat polyclonal antibodies against Gli3 (1:250, R&D). The same membranes were probed with a 1:5000 dilution of anti-β-actin monoclonal antibody (Millipore) to ensure equal loading of cell protein per lane. All blots were incubated with 1:2500 dilutions of secondary horseradish peroxidase-conjugated anti-mouse or anti-goat antibody (DAKO). Antibody-bound proteins were visualized using a chemiluminescence system (Amersham Pharmacia Biotech). The representative pictures of at least 3 independent assays were shown.

RNA Sequencing

Bulk and single-cell (sc) RNA sequencing were performed at the Centre of Genomic Science, The University of Hong Kong. For scRNA-seq, the Smart-seq® v4 (Clontech) kit was used for first-strand synthesis. Single cells were directly sorted into 4 μl of lysis buffer in a 384-well plate using a FACSAria III flow cytometer (BD Biosciences). First-strand DNA was synthesized within 16 cycles of amplification according to the manufacturer's instructions. cDNA was purified on Agencourt AMPureXP magnetic beads, washed twice with fresh 80% ethanol and eluted in 17 μl of elution buffer. Then, 1 μl of cDNA was checked and quantified on an Agilent Bioanalyzer high-sensitivity DNA chip. Sequencing libraries were produced using Illumina Nextera XT tagmentation according to the manufacturer's instructions except using 150 pg of input cDNA, 5 min of tagmentation and 12 cycles of amplification using the Illumina XT 24 index primer kit. Libraries were cleaned using an equal volume (50 ml) of Agencourt AMPureXP magnetic beads and re-suspended in 20 μl of elution buffer. Libraries were checked and quantified on an Agilent Bioanalyzer high-sensitivity DNA chip (size range 150-2000 bp) and by Qubit dsDNA BR (Molecular Probes). Libraries were pooled to a normalized concentration of 1.5 nM and sequenced on an Illumina™ NextSeq 500 using the 150 bp paired-end kit as per the manufacturer's instructions.

Computational Analysis Bulk RNAseq Data Analysis

Fastq files were aligned to the ENSEMBL GRCh38 (release 90, https://www.ensembl.org/) human transcriptome using Bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012) and the expression of genes were quantified using TPM value calculated by RSEM v1.3.0 (Li and Dewey, 2011). The R environment (https://www.r-project.org/) was used for the statistical analysis of the data. The differential expression (DE) analyses were performed using DESeq2 v1.20.0 (Love et al., 2014). DEGs (differential expression genes) were identified if they had a Benjamini-Hochberg adjusted p-value less than 0.05 and a log₂(TPM +1) greater than 1.5 or less than −1.5. Spearman correlation between the bulk RNA samples were calculated using R stats v3.4.3 package. Gene ontology (GO) functional enrichment analysis was performed by WebGestalt (Wang et al., 2017) package using Gene Set Enrichment Analysis (GSEA) method. GO terms with an FDR value below 0.05 and an adjusted p-value less than 0.01 were selected as significant GO terms.

Single Cell RNA Sequencing Data Analysis

Fastq files with paired-end reads were aligned to the ENSEMBL GRCh38 (release 90, https://www.ensembl.org/) human transcriptome using Bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012) with options ‘—sensitive—mp 1,1—np 1—score-min L,0,-0.1-I 1-X 2000—no-mixed—no-discordant-N 1-L 25-k 200’ which allows one mismatch during sequence alignment. Quality control of the reads of each cell was assessed using FastQC v0.11.6 (FIG. 8). Gene expression level was quantified using TPM values generated by RSEM v1.3.0 (Li and Dewey, 2011). For the quality control of the genes and cells, genes which were undetected in all cells and cells which expressed with either fewer than 3,000 genes or more than 9,000 genes were excluded from the expression matrix for downstream analysis (FIG. 8). Distribution of reads count and detected gene number in the cells and fitted sequencing saturation curve are shown in FIG. 8. Highly variable genes were selected by fitting a generalized linear noise model (implement by scikit-learn v0.19.1 python module) to the largest difference between the observed coefficient of variation (CV) and the predicted CV (La Manno et al., 2016).

Outlier Detection and Cell Clustering

Since cell outliers can severely affect the clustering, DEG and gene co-expression analysis (FIG. 16 A), Applicant first remove the cells that far away from any other cells in the cell population as the method described below. Firstly, dimension reduction was performed by PCA analysis to reduce the effect of the noise genes; then mahalanobis distance between each cell was calculated based on the top 99% variance explained PCs. The distance between a cell and its kth nearest neighbors was calculated using the following formula:

$\left( {Distance}_{{kth}\mspace{14mu}{nearest}\mspace{14mu}{neighbors}} \right)_{i} = \frac{\sum_{j = k}^{j = {k + n}}\left( {Distance}_{mahalanobis} \right)_{ij}}{n}$

where i is the ith cells, n is the sample size to collect, j is the jth nearest neighbor. Cell has the top 5% largest Distance_(kth nearest neighbors) will be considered as outlier. This method can robustly remove the simulated outliers and keep the rare subgroups which performs better than existing tool (eg. mvoutlier) as shown in FIGS. 16 B and 16 C.

After removing the outliers, SC3 v1.7.7 (Kiselev et al., 2017) was used to cluster the cells using the top 6,000 highly variable genes. Markers of each cluster (FIG. 9) were identified by the get_marker_genes( )function implement in SC3. The expressions of the markers were visualized in the form of violin plot by ggplot2.

PCA, t-SNE and SPRING Visualization

Three different methods were used to visualize single-cell RNA-seq data. All 17255 protein-coding genes detected in cells were used to perform the visualization (FIG. 17). Feature selection was not performed in this step; thus, less bias was introduced in the visualization. The same pattern was found in all three visualization results as shown in FIG. 10. PCA and t-SNE were performed using prcomp and Rtsne R package (Version 3.5.0). SPRING visualization was performed as described in the previous paper (Weinreb et al., 2018).

Proliferation and Migration Index

To estimate the proliferation and migration rate of each cell based on the gene expression pattern, Applicant built a LASSO linear regression model using the expression data of the cell cycle and migration-related genes and assigned each cell a score between 0 to 1 (1 when a cell had a high proliferation/migration rate and 0 when it did not) respectively as described in previous paper (La Manno et al., 2016). To implement the model, cell cycle genes were selected from the PANTHER GO database, migration-related genes were obtained from Morrison's paper (Morrison et al., 2017). Irrelevant genes were filtered out by setting a correlation threshold. As the cells would span across dividing and non-dividing/migrating and non-migrating states, K-means clustering was performed to separate the two subgroups. Finally, these two subgroups were used to train the linear regression model with L1-norm regularization and proliferation/migration rate were predicted for each cell based on the expression data of the selected genes respectively.

Single Cell Pseudotime Analysis

SPRING (Weinreb et al., 2018) algorithm can robustly capture complex population topologies in scRNA-seq data by Force-directed k-nearest-neighbor graphs. After all the cells were ordered by SPRING method, a smooth curve was fitted across the developmental path by principal.curve (R package). Before curve fitting, outliers were removed by the method described previously. Then, all the cells were projected to the smooth curve. The pseudotime of a cell is the distance of their projection point to the beginning of the curve. Finally, the pseudotime of all cells were normalized to [0, 1].

DEG and Gene Co-Expression Network Analysis

DEG analysis was performed by SCDE (Kharchenko et al., 2014). GO and KEGG annotations were performed by clusterProfiler R package (Yu et al., 2012). The gene co-expression network (FIG. 4H) was constructed by WGCNA (Langfelder and Horvath, 2008) according to the correlation of the genes. Genes were selected as the overlapping of the TFs in the new markers of the eight clusters. The gene co-expression network was visualized by Cytoscape software.

All annotated code showing key steps of the analysis are available on GitHub at: https://github.com/ellylab/HCO-paper.

In vitro differentiation of ENCCs to ENS neurons

Around 40 thousand FACS-enriched NC cells were seeded as droplets on poly-ornithine/laminin/fibronectin (PO/LM/FN)-coated 24 well plate in N2 medium containing 10 ng/ml FGF2, 3 μM CHIR99021 and 10 μM Y-27632. The neuronal differentiation started 48 hours later and the attached NC cells were then cultured with N2 medium containing BDNF (10 ng ml⁻¹ PeproTech, 450-01), GDNF (10 ng ml⁻¹, Peprotech, 450-10) and ascorbic acid (200 μM, Sigma, A4034-100G), NT-3 (10 ng ml⁻¹, PeproTech, 450-03), NGF (10 ng ml⁻¹, PeproTech, 450-01) and cAMP (1 μM, Sigma, D0260). The culture medium was changed every 2 days. NC-derived neurons at differentiation days 21 and 32 were fixed for immunocytochemistry analyzes and harvested using Accutase for scRNA sequencing, respectively.

Derivation of HCOs from hPSCs

Cells were fed mTeSR1 media and routinely passaged using Dispase II (Gibco). ENCC were generated as described above, and HCOs were generated according to a published protocol (Munera et al., 2017). ENCC and HCOs were then combined at an early stage of colon differentiation to generate HCOs containing nerve cells (FIG. 6A). Briefly, for induction of definitive endoderm (DE), hPSC were passaged with Accutase (Invitrogen) and plated at a density of 100,000 cells per well in a Matrigel-coated, Nunclon surface 24-well plate. For Accutase-split cells, 10 μM Y-27632 compound (Sigma) was added to the media for the first day. After the first day, the medium was changed to mTeSR1, and cells were grown for an additional 24 hr. Cells were treated with 100 ng/mL of Activin A for 3 days, and DE was then cultured in hindgut induction medium (RPMI 1640, 2 mM L-glutamine, 2% decomplemented FBS and penicillin-streptomycin) for 4 days with 500 ng/mL FGF4 (R&D) and 2 μM CHIR99021 (Tocris) to induce formation of mid-hindgut spheroids. Spheroids were collected from 24-well plates, pooled, mixed with 5,000 FACS-sorted ENCCs, and plated in Matrigel (BD) at a minimum of 30 spheroids per well. To generate HCOs, spheroids were overlaid with 100 ng/mL EGF plus 100 ng/mL BMP2 (R&D) for 3 days. The medium was then changed twice weekly thereafter. HCOs were replated in fresh Matrigel every 5-7 days at a density of 5-10 organoids per well. Cultures were fed a basic gut medium (advanced DMEM/F12, 1×B27 supplement, 1×N2 supplement, 10 μM HEPES, 2 mM 1-glutamine, 1×Pen-Strep) supplemented with 100 ng EGF ml-1 and maintained in vitro for up to 8 weeks.

In vivo transplantation, electrical-field stimulation and ex vivo neuromuscular coupling test of HCOs

HCOs+ENCCs were ectopically transplanted into the kidney capsule of NOD/SCID mice following a previously developed protocol(Workman et al., 2017). Briefly, 5-8-week-old HCOs were embedded in collagen and transplanted into the kidney subcapsular space. Engrafted HCOs were harvested 8-10 weeks after transplantation and either analyzed for neural and glial markers or used for electrical-field stimulation (EFS) experiments and ex vivo neuromuscular coupling tests. For EFS, HCOs, HCOs+ENCCs and HCOs+SAG-ENCCs were explanted into Tyrode's solution and equilibrated for approximately 5 min before stimulation was begun. Electric stimulation was applied using a Grass S88 Stimulator (Grass Technologies) with 2-3 pulses, 5-ms duration and 30 V settings. HCO, HCOs+ENCCs and HCOs+SAG-ENCCs were then incubated for 5 min in 10 μM Tetrodotoxin (TTX) diluted in Tyrode's, rinsed and placed back in fresh Tyrode's. EFS was then repeated. Videos were recorded on a Leica dissection microscope using Leica Application Suite software and processed with VideoLAN and Handbrake to achieve 16× play speed. Videos were analyzed using the video-analysis software Tracker version 4.91 (Douglas Brown). Automated point tracking with position was performed to measure the movement within explanted HCOs, HCOs+ENCCs and HCOs+SAG-ENCCs during EFS.

For ex vivo neuromuscular coupling test, engrafted HCOs, HCOs+ENCCs and HCOs+SAG-ENCCs were harvested and placed in ice-cold HBSS. Muscle strips (4-6 mm in length and 1-2 mm in width) were cut from the engrafted HCOs, HCOs+ENCCs and HCOs+SAG-ENCCs. Preparations were suspended isometric-force organ-bath chambers filled with Krebs solution (117 mM NaCl; 4.7 mM KCl; 1.2 mM MgCl₂; 1.2 mM NaH₂PO₄; 25 mM NaHCO₃; 2.5 mM CaCl₂, and 11 mM glucose), warmed at 37° C. and with 95% O₂+5% CO₂. After an equilibration period of 60 min, the contractile response of the muscle was continuously recorded, using a four-chamber tissue-organ bath with isometric-force transducers (AD Instruments) coupled to a computer equipped with LabChart Pro software (AD Instruments). Muscle preparations were stimulated with dimethylphenylpiperazinium (DMPP; 10 μM; Sigma-Aldrich). Chemical stimulations were applied at 15-min intervals and followed by three washes. TTX (10 μM) was applied 5 min before DMPP stimulation. The effects of chemical stimulation on tension were evaluated by measuring the area under the curve (AUC). Data are expressed in ΔAUC, i.e., “stimulated” AUC measured 120 s after stimulation minus “control” AUC measured 120 s before stimulation.

Immunofluorescence Analysis

For immunocytochemistry, the cells were fixed with 4% paraformaldehyde in PBS at room temperature for 30 min, followed by blocking with 1% bovine serum albumin (BSA) (Thermo Scientific, 23209) with or without 0.1% Triton X-100 (Sigma, T8787) in PBS buffer. Cells were then incubated in primary antibody overnight at 4° C. and host-appropriate Alexa Fluor −488 or 594 secondary antibody (Molecular Probes, Invitrogen) for 1 h at room temperature. Cells were then counterstained with mounting medium with DAPI (Thermo Scientific, P36931) to detect nuclei. Cells were photographed using Carl Zeiss confocal microscope (LSM 800). Quantitative image analysis of differentiated neuronal cultures was performed with ImageJ. A minimum of 4,000 cells were analyzed per sample. Percentages of neuronal cells were measured over the total number of cells (DAPI) and the values reported in bar charts represent the mean ±SEM.

For section immunohistochemistry, the innervated HCO and HCO explants were fixed in 4% paraformaldehyde (PFA) in PBS at 4° C., dehydrated and cryoprotected in 30% sucrose in PBS at 4° C. or dehydrated with ethanol series, and embedded in OCT compound (Tissue-Tek) or paraffin, respectively. The sections were rehydrated using standard protocols and microwaved for 15 min in target antigen retrieval buffer (Abcam). The sections were then blocked in PBS containing 5% normal donkey serum (Sigma) with 0.5% Trition-X for 1 hour at room temperature, then incubated overnight at 4° C. in a mixture of the anti-human antibodies against various colon and neuronal markers. After washing, the immunosignals were then detected using the secondary antibody conjugated with Alexa Fluor 488, 594, 647 (Invitrogen). Sections were photographed using a Carl Zeiss LSM780 or LSM810 confocal microscope.

Media

The NCC induction medium may contain knockout Dulbecco's Modified Eagle Medium (DMEM) plus 15% Knockout Serum Replacement (KSR) (Life Technologies, 10828-028), NEAA (Life Technologies, 11140-050), L-glutamine (Life Technologies, 25030-081), β-mercaptoethanol (Life Technologies, 21985-023), LDN193189 (100 nM, Stemgent) and SB431542 (10 μM, Tocris). The dual SMAD inhibitors and a potent GSK inhibitor may be added at different point in time during NC induction, such as, for example, including LDN193189 (from day 0 to day 3), SB431542 (from day 0 to day 4), 3 μM CHIR99021 (from day 2 to day 10, Tocris Bioscience, 4423). The NC cells may be caudalized with 1 μM retinoic acid (from day 6 to day 9). The KSR medium may gradually be changed to N2 medium at day 4 by increasing N2 from 25% to 75% from day 4 to 9 as described previously (Lai et al., 2017). N2 medium may contain neural basal medium (Life Technologies, 22103-049) and DMEM/F12 (Life Technologies, 10565-018 (1:1), N2 supplement (Life Technologies, 17502-048), B27 supplement (Life Technologies, 17504-044) and insulin (Life Technologies, 12585-014).

NCC Induction Medium Example

Knockout DMEM plus 15% KSR (1 mM, Life Technologies, 10828-028), NEAA (Life Technologies, 11140-050), L-glutamine (2 mM, Life Technologies, 25030-081), β-mercaptoethanol (55 μM, Life Technologies, 21985-023), LDN193189 (100 nM, Stemgent) and SB431542 (10 μM, Tocris). (The dual SMAD inhibitors and a potent GSK inhibitor were added at different time frame during the NC induction, including LDN193189 (from day 0 to day 3), SB431542 (from day 0 to day 4), 3 μM CHIR99021 (from day 2 to day 10, Tocris Bioscience, 4423). The NC cells may be finally caudalized with 1 μM retinoic acid (from day 6 to day 9). The KSR medium may be gradually changed to N2 medium at day 4 by increasing N2 from 25% to 75% from day 4 to 9 as described previously (Lai et al., 2017).

The N2 medium may contain neural basal medium (Life Technologies, 22103-049) and DMEM/F12 (Life Technologies, 10565-018 (1:1), N2 supplement (Life Technologies, 17502-048), B27 supplement (Life Technologies, 17504-044) and insulin (Life Technologies, 12585-014).

References

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All percentages and ratios are calculated by weight unless otherwise indicated.

All percentages and ratios are calculated based on the total composition unless otherwise indicated.

It should be understood that every maximum numerical limitation given throughout this specification includes every lower numerical limitation, as if such lower numerical limitations were expressly written herein. Every minimum numerical limitation given throughout this specification will include every higher numerical limitation, as if such higher numerical limitations were expressly written herein. Every numerical range given throughout this specification will include every narrower numerical range that falls within such broader numerical range, as if such narrower numerical ranges were all expressly written herein.

The dimensions and values disclosed herein are not to be understood as being strictly limited to the exact numerical values recited. Instead, unless otherwise specified, each such dimension is intended to mean both the recited value and a functionally equivalent range surrounding that value. For example, a dimension disclosed as “20 mm” is intended to mean “about 20 mm.”

Every document cited herein, including any cross referenced or related patent or application, is hereby incorporated herein by reference in its entirety unless expressly excluded or otherwise limited. The citation of any document is not an admission that it is prior art with respect to any invention disclosed or claimed herein or that it alone, or in any combination with any other reference or references, teaches, suggests or discloses any such invention. Further, to the extent that any meaning or definition of a term in this document conflicts with any meaning or definition of the same term in a document incorporated by reference, the meaning or definition assigned to that term in this document shall govern.

While particular embodiments of the present invention have been illustrated and described, it would be obvious to those skilled in the art that various other changes and modifications may be made without departing from the spirit and scope of the invention. It is therefore intended to cover in the appended claims all such changes and modifications that are within the scope of this invention. 

1. An in vitro method of differentiating a precursor cell into a neural crest cell (NCC), comprising activating a Hedgehog signaling pathway (“HH signaling pathway”) in said precursor cell, wherein said precursor cell is contacted with a neural crest cell (“NCC”) induction medium until said precursor cell differentiates into said neural crest cell.
 2. The method of claim 1, wherein said precursor cell is a pluripotent stem cell.
 3. The method of claim 1, wherein said HH signaling pathway activation is from about day 0 to about day 4 of said contacting step, or from about day 0 to about day 10 of said contacting step.
 4. The method of claim 1, wherein activation of said HH signaling pathway comprises contacting said precursor cell with one or both of an HH agonist and an HH antagonist that acts as a partial agonist.
 5. The method of claim 1, wherein said NCC is derived in the absence of SMOOTHENED agonist (SAG) and wherein said NCC is characterized by elevated expression of p75^(NTR), HNK1, RET, TFAP2B, SNAI1, SNAI2, SOX10 expression, and/or expression of an enteric HOX code, wherein expression of an enteric HOX code is selected from expression of one or more of HOXB3, HOXB4, and HOXB5.
 6. The method of claim 1, wherein said precursor cell is a population of precursor cells, wherein said method provides a substantially homogenous population of NCCs primed to a neurogenic lineage.
 7. The method of claim 1, wherein said NCC is capable of differentiation into other non-neurogenic lineages.
 8. The method of claim 4, wherein said HH agonist, said HH antagonist that acts as a partial agonist, or combination thereof, is contacted with said precursor cell from day 0 to day 10 of said contacting step, or from day 0 to about day 4, or about day 4 to about day
 10. 9. The method of claim 1, wherein said precursor cell is contacted with an HH activator for a period of time sufficient to increase the number of SOX2+NANOG-cells.
 10. A method of making an innervated colonic organoid model, comprising the step of a. contacting an enteric NCC (ENCC) primed to a neurogenic lineage of claim 1 with a hindgut spheroid; and b. transplanting said hindgut spheroid and said ENCCs primed to a neurogenic lineage into a kidney capsule of an immunodeficient host until innervated colonic organoid forms; wherein said hindgut spheroid is obtained from definitive endoderm.
 11. The method of claim 10, wherein said innervated colonic organoid comprises NC cells differentiated into neurons, wherein said innervated colonic organoid is characterized by the formation of crypts and colonic epithelium and nerve cells, wherein said nerve cells are selected from TUJ1+ neurons, S100b+glia, and combinations thereof.
 12. The method of claim 10, wherein said innervated colonic organoid is characterized by expression of one or markers selected from gut epithelium (CDH1+), colon (SATB2+), goblet (MUC2+), endocrine (GLP1+)-like cells, or a combination thereof.
 13. The method of claim 1, wherein said neural crest cell induction medium comprises a) knockout Dulbecco's Modified Eagle Medium (“DMEM”) and Knockout Serum Replacement (“KSR); b) L-glutamine; c) β-mercaptoethanol; and d) LDN193189.
 14. The method of claim 13, wherein said neural crest cell induction medium comprises CHIR99021 and/or retinoic acid.
 15. (canceled).
 16. An innervated human colonic organoid (HCO) comprising hPSC-derived NCCs, wherein said hPSC-derived NCCs are derived from a precursor cell contacted with an HH signaling pathway activator, and a gut endodermal cell.
 17. The innervated HCO of claim 16, wherein greater than about 50% of neurons are mature enteric neurons expressing Calretinin, Protein Gene Product 9.5 (PGP9.5±) and neurofilament (NFL+).
 18. The innervated HCO of claim 16, wherein said ENCC cell is an ENCCSAG0_10.
 19. The innervated HCO of claim 16, wherein said innervated HCO comprises cells from two or more individuals.
 20. The innervated HCO of claim 16, wherein said innervated HCO comprise increased numbers of mature neurons (PGP9.5+, NFL+) as compared to an innervated HCO that is not treated with an HH agonist. 21.-22. (canceled)
 23. The method of claim 4, wherein said HH agonist is selected from a SMOOTHENED agonist (“SAG”). recombinant Some Hedgehog (Shh), Purmorphamine, and combinations thereof; and/or wherein said HH antagonist that acts as a partial agonist is selected from Cyclopamine, Vismodegib (GDC-0449), and combinations thereof.
 24. The method of claim 1, wherein said NCCs have elevated expression of neuronal progenitor markers (TUBB3), loss of SOX10 expression, and co-expression of an enteric HOX code (HOXB3+, HOXB4+, HOXB5+); wherein said, NC cells are SOX10⁻, PHOX2B³⁰ , TBB3^(high) (Cluster 6 and 7); wherein said NC cells are TUBB3^(high), ELAVL4+(Cluster 8); and/or wherein said NC cells have reduced expression of NC markers TFAP2A, SNAIL, and SOX10 and elevated expression of neurogenic markers TUBB3, ELVA4, PHOX2B. 